Candidate loci

https://www.ncbi.nlm.nih.gov/nuccore/?term=Cannabis%20ALT4

https://www.ncbi.nlm.nih.gov/search/all/?term=Cannabis%20BKR

Methods

Genome Wide Association Study

In order to discover variants associated with the varin phenotype, a Genome Wide Association Study (GWAS) was performed using GAPIT3 (https://doi.org/10.1016/j.gpb.2021.08.005). The varin data was ordered quantile (ORQ) normalization transformed using the ‘bestNormalize::orderNorm()’ function (10.32614/RJ-2021-041; 10.1080/02664763.2019.1630372) to improve normalcy. Genotypic data in the VCF format (https://doi.org/10.1093/bioinformatics/btr330) was imported into R (https://www.R-project.org/) using vcfR (https://doi.org/10.1111/1755-0998.12549) and converted to hapmap format using vcfR::vcfR2hapmap(). The ordered quantile normalized phenotypes and the hapmap format genotypes were used for GWAS using the function GAPIT::GAPIT() and the options PCA.total = 6 and model = “Blink”. The Blink model begins with a simple model where the phenotype is described as a function of the dosage of the alternate allele in the genotypes. These are sorted by p-value. The first variant is selected subsequent loci that are determined to be in linkage disequilibrium with the first are removed. This is iterated through subsequent variants until the remaining variants are all organized by linkage. Detail on the Blink method can be found in it’s publication (https://doi.org/10.1093/gigascience/giy154).

Figure X. Manhattan plot exploring genome wide genotype association with the phenotypic trait ‘varin content’. Points indicated the genomic location and significance of association for each variant. The size and transparency of each point was scaled by it’s significance.

Phenotypes

PCA

A caption

A caption

Manhattan plots

## [1] "pca3_BLINK.Varin_Total"       "pca6_BLINK.Varin_Total"      
## [3] "pca6_Blink, OrderNorm_Varin"  "pca9_BLINK.Varin_Total"      
## [5] "pca10_BLINK, Varin"           "pca10_BLINK, OrderNorm_Varin"
## [7] "pca20_BLINK.Varin_Total"
## [1] TRUE

Table X. Select results from GAPIT GWAS using the Blink model, sorted by P.value.
SNP P.value -log10(P) MAF nobs H.B.P.Value Effect POS Pos
EH23b.chr8_44780947 0.0e+00 21.894262 0.3759259 270 0.0000000 -13.434320 576113361 44780947
EH23b.chr4_43500849 0.0e+00 8.418312 0.3500000 270 0.0001780 5.167570 271185475 43500849
EH23b.chr7_498071 0.0e+00 7.774597 0.4481481 270 0.0005223 2.532142 467617985 498071
EH23b.chr3_54125016 1.0e-07 7.108520 0.3981481 270 0.0015289 6.260843 198004642 54125016
EH23b.chr4_6356002 1.0e-07 7.086308 0.4962963 270 0.0015289 -4.041236 234040628 6356002
EH23b.chr6_42100569 4.0e-07 6.420980 0.4592593 270 0.0051487 5.957177 429207705 42100569
EH23b.chr5_15864046 4.0e-07 6.412860 0.4962963 270 0.0051487 6.447545 324682182 15864046
EH23b.chr4_65316473 3.9e-06 5.410251 0.3537037 270 0.0453224 -3.713511 293001099 65316473
EH23b.chr3_52792408 4.9e-06 5.305762 0.3981481 270 0.0512447 6.098214 196672034 52792408
EH23b.chr4_16520435 9.0e-06 5.047746 0.4944444 270 0.0835424 -4.630612 244205061 16520435

Loop

PCA = 6

## [1]  20 255
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